I have a question regarding to account for batch differences in RNA-seq data analysis.
Originally, an RNA SEQ data set was sequenced with two conditions (Day 0, Day 30), and then a couple months later we sequenced another data set (Day 30, Day 90). I now want to analyse the full data set (Day 0, Day 30, and Day 90). However, I am having trouble understanding how to account for batch differences. When I look at the raw dataset, the main issue to me is that my two data sets contain different row numbers (batch 1 = 583400, batch2= 63682). I was told to use ComBat-SEQ, but I am really lost with this.
If anybody could point me in the right direction I'd be really grateful!